How to implement batch training? about pygat

[HowardZorn]

Looking forward to seeing your progress bro.

Hello, Shuyue

My solution is under review now. You can see it at Pull Requests#63, or visit my branch: HowardZorn/pyGAT.

Cheers,
Howard

[HowardZorn]

The memory usage is just too high to use batch training. The input with shape batch_size × node × in_features would be expanded to shape batch_size × node × node × 2 out_features during training. I'm trying to reduce the memory usage.

[HowardZorn]

Dear Shuyue,

I'm glad to see your reply.

Meanwhile, can you help me review and check the codes to make sure they worked correctly, I mean, mathematically?

Your implementation is consistent with the algorithm in the original paper, and so am I. I don't think there is anything wrong.

I also found that the memory usage surged while training with batches.
The memory issue of this model really bothers me.
Do you have any ideas to further decrease memory usage and speed up the training process?

I also suffered from this. Finally, I lowered the hyperparameters to avoid OOM errors. I will continue to find some ways to reduce memory usage from the algorithm.

Cheers,
Howard

[SuperBruceJia]

The memory usage is just too high to use batch training. The input with shape batch_size × node × in_features would be expanded to shape batch_size × node × node × 2 out_features during training. I'm trying to reduce the memory usage.

I'm really looking forward to your solution to memory usage!
Thanks in advance.

Best,

Shuyue

[SuperBruceJia]

The memory usage is just too high to use batch training. The input with shape batch_size × node × in_features would be expanded to shape batch_size × node × node × 2 out_features during training. I'm trying to reduce the memory usage.

I also met critical memory usage problems while implementing on a large-number nodes dataset, e.g., 5000 - 10000 nodes. I really hope you can solve the memory problem bro.

Looking forward to seeing your progress bro.

Best regards,

Shuyue

[SuperBruceJia]

@Diego999 @HowardZorn @pbloem @sh0416

[HowardZorn]

Actually, implementing batch training is not a hard work if memory is sufficient during training. Here is an example: https://blog.csdn.net/pixian3729/article/details/110261140 (In Simplified Chinese). Good luck!

[SuperBruceJia]

Looking forward to seeing your progress bro.

Hello, Shuyue

My solution is under review now. You can see it at Pull Requests#63, or visit my branch: HowardZorn/pyGAT.

Cheers,
Howard

Dear Howard,

Thanks a lot for your help! You are an extraordinary man! I really appreciate it.

Another thing to inquire about is the multi-GPU training, when I try to use two GPUs, an error about the model and data parallel occurred.

For details:

  File "/home/jsy/.conda/envs/torch/lib/python3.8/site-packages/torch/nn/modules/module.py", line 727, in _call_impl
    result = self.forward(*input, **kwargs)
  File "/home/jsy/.conda/envs/torch/lib/python3.8/site-packages/torch/nn/parallel/data_parallel.py", line 161, in forward
    outputs = self.parallel_apply(replicas, inputs, kwargs)
  File "/home/jsy/.conda/envs/torch/lib/python3.8/site-packages/torch/nn/parallel/data_parallel.py", line 171, in parallel_apply
    return parallel_apply(replicas, inputs, kwargs, self.device_ids[:len(replicas)])
  File "/home/jsy/.conda/envs/torch/lib/python3.8/site-packages/torch/nn/parallel/parallel_apply.py", line 86, in parallel_apply
    output.reraise()
  File "/home/jsy/.conda/envs/torch/lib/python3.8/site-packages/torch/_utils.py", line 428, in reraise
    raise self.exc_type(msg)
RuntimeError: Caught RuntimeError in replica 0 on device 0.
Original Traceback (most recent call last):
  File "/home/jsy/.conda/envs/torch/lib/python3.8/site-packages/torch/nn/parallel/parallel_apply.py", line 61, in _worker
    output = module(*input, **kwargs)
  File "/home/jsy/.conda/envs/torch/lib/python3.8/site-packages/torch/nn/modules/module.py", line 727, in _call_impl
    result = self.forward(*input, **kwargs)
  File "/home/jsy/gnn/gnn.py", line 32, in forward
    x = torch.cat([att(x, adj) for att in self.attentions], dim=1)
  File "/home/jsy/gnn/gnn.py", line 32, in <listcomp>
    x = torch.cat([att(x, adj) for att in self.attentions], dim=1)
  File "/home/jsy/.conda/envs/torch/lib/python3.8/site-packages/torch/nn/modules/module.py", line 727, in _call_impl
    result = self.forward(*input, **kwargs)
  File "/home/jsy/gnn/layers.py", line 32, in forward
    attention = torch.where(adj > 0, e, zero_vec)
RuntimeError: The size of tensor a (3000) must match the size of tensor b (1500) at non-singleton dimension 1

Thanks in advance and I'm looking forward to your reply.

Best regards,

Shuyue

@HowardZorn @Diego999

[HowardZorn]

Another thing to inquire about is the multi-GPU training, when I try to use two GPUs, an error about the model and data parallel occurred.

Shuyue, happy to see your reply. Multi-GPU training must implement batch training. My solution is just for memory issues. Could you show your code for batch training?

[SuperBruceJia]

Another thing to inquire about is the multi-GPU training, when I try to use two GPUs, an error about the model and data parallel occurred.

Shuyue, happy to see your reply. Multi-GPU training must implement batch training. My solution is just for memory issues. Could you show your code for batch training?

Dear Howard,

Thanks a lot for your quick reply.

As for the batch training, please refer to this issue #36.

Best,

Shuyue

[SuperBruceJia]

@HowardZorn

[SuperBruceJia]

Another thing to inquire about is the multi-GPU training, when I try to use two GPUs, an error about the model and data parallel occurred.

Shuyue, happy to see your reply. Multi-GPU training must implement batch training. My solution is just for memory issues. Could you show your code for batch training?

Dear Howard,

If you don't mind, you can upload and pull the batch training with less memory usage codes.

Thanks in advance.

Best,

Shuyue

[SuperBruceJia]

@HowardZorn

[SuperBruceJia]

Another thing to inquire about is the multi-GPU training, when I try to use two GPUs, an error about the model and data parallel occurred.

Shuyue, happy to see your reply. Multi-GPU training must implement batch training. My solution is just for memory issues. Could you show your code for batch training?

Dear Howard,

Thanks a lot for your help.

I edited the batch training codes:

---

At the layers.py file:

class GraphAttentionLayer(nn.Module):
    """
    https://github.com/Diego999/pyGAT/blob/master/layers.py
    Simple GAT layer, similar to https://arxiv.org/abs/1710.10903
    """
    def __init__(self, in_features, out_features, dropout, alpha, concat=True):
        super(GraphAttentionLayer, self).__init__()
        self.dropout = dropout
        self.in_features = in_features
        self.out_features = out_features
        self.alpha = alpha
        self.concat = concat

        self.W = nn.Parameter(torch.empty(size=(in_features, out_features)))
        nn.init.xavier_uniform_(self.W.data, gain=1.414)

        self.a = nn.Parameter(torch.empty(size=(2 * out_features, 1)))
        nn.init.xavier_uniform_(self.a.data, gain=1.414)

        self.leakyrelu = nn.LeakyReLU(self.alpha)

    def forward(self, h, adj):
        """
        :param h: (batch_zize, number_nodes, in_features)
        :param adj: (batch_size, number_nodes, number_nodes)
        :return: (batch_zize, number_nodes, out_features)
        """
        # batchwise matrix multiplication
        Wh = torch.matmul(h, self.W)  # (batch_zize, number_nodes, in_features) * (in_features, out_features) -> (batch_zize, number_nodes, out_features)
        e = self.prepare_batch(Wh)  # (batch_zize, number_nodes, number_nodes)

        # (batch_zize, number_nodes, number_nodes)
        zero_vec = -9e15 * torch.ones_like(e)

        # (batch_zize, number_nodes, number_nodes)
        attention = torch.where(adj > 0, e, zero_vec)

        # (batch_zize, number_nodes, number_nodes)
        attention = F.softmax(attention, dim=-1)

        # (batch_zize, number_nodes, number_nodes)
        attention = F.dropout(attention, self.dropout, training=self.training)

        # batched matrix multiplication (batch_zize, number_nodes, out_features)
        h_prime = torch.matmul(attention, Wh)

        if self.concat:
            return F.elu(h_prime)
        else:
            return h_prime

    def prepare_batch(self, Wh):
        """
        with batch training
        :param Wh: (batch_zize, number_nodes, out_features)
        :return:
        """
        # Wh.shape (B, N, out_feature)
        # self.a.shape (2 * out_feature, 1)
        # Wh1&2.shape (B, N, 1)
        # e.shape (B, N, N)

        B, N, E = Wh.shape  # (B, N, N)

        # (B, N, out_feature) X (out_feature, 1) -> (B, N, 1)
        Wh1 = torch.matmul(Wh, self.a[:self.out_features, :])  # (B, N, out_feature) X (out_feature, 1) -> (B, N, 1)
        Wh2 = torch.matmul(Wh, self.a[self.out_features:, :])  # (B, N, out_feature) X (out_feature, 1) -> (B, N, 1)

        # broadcast add (B, N, 1) + (B, 1, N)
        e = Wh1 + Wh2.permute(0, 2, 1)  # (B, N, N)
        return self.leakyrelu(e)

    def __repr__(self):
        return self.__class__.__name__ + ' (' + str(self.in_features) + ' -> ' + str(self.out_features) + ')'

---

At the same time,
at the models.py file:

We should change line 21: x = torch.cat([att(x, adj) for att in self.attentions], dim=1) to

x = torch.cat([att(x, adj) for att in self.attentions], dim=-1)

Meanwhile, can you help me review and check the codes to make sure they worked correctly, I mean, mathematically?

Thanks in advance and have a nice day!

Best,

Shuyue

@HowardZorn

[SuperBruceJia]

Another thing to inquire about is the multi-GPU training, when I try to use two GPUs, an error about the model and data parallel occurred.

Shuyue, happy to see your reply. Multi-GPU training must implement batch training. My solution is just for memory issues. Could you show your code for batch training?

Dear Howard,

I also found that the memory usage surged while training with batches.
The memory issue of this model really bothers me.
Do you have any ideas to further decrease memory usage and speed up the training process?

I'm looking forward to your reply.

Best,

Shuyue

[SuperBruceJia]

@HowardZorn

[SuperBruceJia]

@Diego999

[SuperBruceJia]

Dear Shuyue,

I'm glad to see your reply.

Meanwhile, can you help me review and check the codes to make sure they worked correctly, I mean, mathematically?

Your implementation is consistent with the algorithm in the original paper, and so am I. I don't think there is anything wrong.

I also found that the memory usage surged while training with batches.
The memory issue of this model really bothers me.
Do you have any ideas to further decrease memory usage and speed up the training process?

I also suffered from this. Finally, I lowered the hyperparameters to avoid OOM errors. I will continue to find some ways to reduce memory usage from the algorithm.

Cheers,
Howard

Great!

Let me try to figure out how to implement on multi GPUs to distribute memories to multiple devices.

Thanks again for your help and guide.

Have a nice day!

Best,

Shuyue

[SuperBruceJia]

Dear Shuyue,

I'm glad to see your reply.

Meanwhile, can you help me review and check the codes to make sure they worked correctly, I mean, mathematically?

Your implementation is consistent with the algorithm in the original paper, and so am I. I don't think there is anything wrong.

I also found that the memory usage surged while training with batches.
The memory issue of this model really bothers me.
Do you have any ideas to further decrease memory usage and speed up the training process?

I also suffered from this. Finally, I lowered the hyperparameters to avoid OOM errors. I will continue to find some ways to reduce memory usage from the algorithm.

Cheers,
Howard

Any idea on this issue? #64

[wpy678]

Another thing to inquire about is the multi-GPU training, when I try to use two GPUs, an error about the model and data parallel occurred.

Shuyue, happy to see your reply. Multi-GPU training must implement batch training. My solution is just for memory issues. Could you show your code for batch training?

Dear Howard,

Thanks a lot for your help.

I edited the batch training codes:

At the layers.py file:

class GraphAttentionLayer(nn.Module):
    """
    https://github.com/Diego999/pyGAT/blob/master/layers.py
    Simple GAT layer, similar to https://arxiv.org/abs/1710.10903
    """
    def __init__(self, in_features, out_features, dropout, alpha, concat=True):
        super(GraphAttentionLayer, self).__init__()
        self.dropout = dropout
        self.in_features = in_features
        self.out_features = out_features
        self.alpha = alpha
        self.concat = concat

        self.W = nn.Parameter(torch.empty(size=(in_features, out_features)))
        nn.init.xavier_uniform_(self.W.data, gain=1.414)

        self.a = nn.Parameter(torch.empty(size=(2 * out_features, 1)))
        nn.init.xavier_uniform_(self.a.data, gain=1.414)

        self.leakyrelu = nn.LeakyReLU(self.alpha)

    def forward(self, h, adj):
        """
        :param h: (batch_zize, number_nodes, in_features)
        :param adj: (batch_size, number_nodes, number_nodes)
        :return: (batch_zize, number_nodes, out_features)
        """
        # batchwise matrix multiplication
        Wh = torch.matmul(h, self.W)  # (batch_zize, number_nodes, in_features) * (in_features, out_features) -> (batch_zize, number_nodes, out_features)
        e = self.prepare_batch(Wh)  # (batch_zize, number_nodes, number_nodes)

        # (batch_zize, number_nodes, number_nodes)
        zero_vec = -9e15 * torch.ones_like(e)

        # (batch_zize, number_nodes, number_nodes)
        attention = torch.where(adj > 0, e, zero_vec)

        # (batch_zize, number_nodes, number_nodes)
        attention = F.softmax(attention, dim=-1)

        # (batch_zize, number_nodes, number_nodes)
        attention = F.dropout(attention, self.dropout, training=self.training)

        # batched matrix multiplication (batch_zize, number_nodes, out_features)
        h_prime = torch.matmul(attention, Wh)

        if self.concat:
            return F.elu(h_prime)
        else:
            return h_prime

    def prepare_batch(self, Wh):
        """
        with batch training
        :param Wh: (batch_zize, number_nodes, out_features)
        :return:
        """
        # Wh.shape (B, N, out_feature)
        # self.a.shape (2 * out_feature, 1)
        # Wh1&2.shape (B, N, 1)
        # e.shape (B, N, N)

        B, N, E = Wh.shape  # (B, N, N)

        # (B, N, out_feature) X (out_feature, 1) -> (B, N, 1)
        Wh1 = torch.matmul(Wh, self.a[:self.out_features, :])  # (B, N, out_feature) X (out_feature, 1) -> (B, N, 1)
        Wh2 = torch.matmul(Wh, self.a[self.out_features:, :])  # (B, N, out_feature) X (out_feature, 1) -> (B, N, 1)

        # broadcast add (B, N, 1) + (B, 1, N)
        e = Wh1 + Wh2.permute(0, 2, 1)  # (B, N, N)
        return self.leakyrelu(e)

    def __repr__(self):
        return self.__class__.__name__ + ' (' + str(self.in_features) + ' -> ' + str(self.out_features) + ')'

At the same time,
at the models.py file:

We should change line 21: x = torch.cat([att(x, adj) for att in self.attentions], dim=1) to

x = torch.cat([att(x, adj) for att in self.attentions], dim=-1)

Meanwhile, can you help me review and check the codes to make sure they worked correctly, I mean, mathematically?

Thanks in advance and have a nice day!

Best,

Shuyue

@HowardZorn

Thank you very much for your sharing

I have also been doing batch training recently

Can you share your code?

[SuperBruceJia]

Another thing to inquire about is the multi-GPU training, when I try to use two GPUs, an error about the model and data parallel occurred.

Shuyue, happy to see your reply. Multi-GPU training must implement batch training. My solution is just for memory issues. Could you show your code for batch training?

Dear Howard,
Thanks a lot for your help.
I edited the batch training codes:
At the layers.py file:

class GraphAttentionLayer(nn.Module):
    """
    https://github.com/Diego999/pyGAT/blob/master/layers.py
    Simple GAT layer, similar to https://arxiv.org/abs/1710.10903
    """
    def __init__(self, in_features, out_features, dropout, alpha, concat=True):
        super(GraphAttentionLayer, self).__init__()
        self.dropout = dropout
        self.in_features = in_features
        self.out_features = out_features
        self.alpha = alpha
        self.concat = concat

        self.W = nn.Parameter(torch.empty(size=(in_features, out_features)))
        nn.init.xavier_uniform_(self.W.data, gain=1.414)

        self.a = nn.Parameter(torch.empty(size=(2 * out_features, 1)))
        nn.init.xavier_uniform_(self.a.data, gain=1.414)

        self.leakyrelu = nn.LeakyReLU(self.alpha)

    def forward(self, h, adj):
        """
        :param h: (batch_zize, number_nodes, in_features)
        :param adj: (batch_size, number_nodes, number_nodes)
        :return: (batch_zize, number_nodes, out_features)
        """
        # batchwise matrix multiplication
        Wh = torch.matmul(h, self.W)  # (batch_zize, number_nodes, in_features) * (in_features, out_features) -> (batch_zize, number_nodes, out_features)
        e = self.prepare_batch(Wh)  # (batch_zize, number_nodes, number_nodes)

        # (batch_zize, number_nodes, number_nodes)
        zero_vec = -9e15 * torch.ones_like(e)

        # (batch_zize, number_nodes, number_nodes)
        attention = torch.where(adj > 0, e, zero_vec)

        # (batch_zize, number_nodes, number_nodes)
        attention = F.softmax(attention, dim=-1)

        # (batch_zize, number_nodes, number_nodes)
        attention = F.dropout(attention, self.dropout, training=self.training)

        # batched matrix multiplication (batch_zize, number_nodes, out_features)
        h_prime = torch.matmul(attention, Wh)

        if self.concat:
            return F.elu(h_prime)
        else:
            return h_prime

    def prepare_batch(self, Wh):
        """
        with batch training
        :param Wh: (batch_zize, number_nodes, out_features)
        :return:
        """
        # Wh.shape (B, N, out_feature)
        # self.a.shape (2 * out_feature, 1)
        # Wh1&2.shape (B, N, 1)
        # e.shape (B, N, N)

        B, N, E = Wh.shape  # (B, N, N)

        # (B, N, out_feature) X (out_feature, 1) -> (B, N, 1)
        Wh1 = torch.matmul(Wh, self.a[:self.out_features, :])  # (B, N, out_feature) X (out_feature, 1) -> (B, N, 1)
        Wh2 = torch.matmul(Wh, self.a[self.out_features:, :])  # (B, N, out_feature) X (out_feature, 1) -> (B, N, 1)

        # broadcast add (B, N, 1) + (B, 1, N)
        e = Wh1 + Wh2.permute(0, 2, 1)  # (B, N, N)
        return self.leakyrelu(e)

    def __repr__(self):
        return self.__class__.__name__ + ' (' + str(self.in_features) + ' -> ' + str(self.out_features) + ')'

At the same time,
at the models.py file:
We should change line 21: x = torch.cat([att(x, adj) for att in self.attentions], dim=1) to

x = torch.cat([att(x, adj) for att in self.attentions], dim=-1)

Meanwhile, can you help me review and check the codes to make sure they worked correctly, I mean, mathematically?
Thanks in advance and have a nice day!
Best,
Shuyue
@HowardZorn

Thank you very much for your sharing

I have also been doing batch training recently

Can you share your code?

Hi,

Thanks for your interest!

I'm currently working on cross-subject research rather than GNN.
As a result, the codes didn't fit the GNN datasets, e.g., the Cora dataset.

However, after I finished the project, if there are superior performances, I'll open-source the codes.
I'll let you know later.

Best regards,

Shuyue

[HowardZorn]

I also found that the memory usage surged while training with batches.
The memory issue of this model really bothers me.
Do you have any ideas to further decrease memory usage and speed up the training process?

I found that the multi-head attention implementation of pyGAT could be improved.

[SuperBruceJia]

I also found that the memory usage surged while training with batches.
The memory issue of this model really bothers me.
Do you have any ideas to further decrease memory usage and speed up the training process?

I found that the multi-head attention implementation of pyGAT could be improved.

Dear Howard,

Could your share your codes or ideas?

Thanks in advance.

Best,

Shuyue

[SuperBruceJia]

@HowardZorn